Database Record
Soybean Knowledge Base: SoyKB
| IDNBDC common database IDs, which should be written in parentheses if there are multiple titles, such as Japanese and English. | NBDC01917 | ||||
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| Database nameName of the database | Soybean Knowledge Base | ||||
| Alternative nameAlternative name of the database | SoyKB | ||||
| URLURL of the database | http://soykb.org/ | ||||
| Database maintenance siteSite maintaining the database | University of Missouri | ||||
| Country/RegionCountry or region name where the database maintenance site is located | United States | ||||
| Database descriptionDatabase descirption | Soybean Knowledge Base (SoyKB), is a comprehensive all-inclusive web resource developed for soybean translational genomics and molecular breeding. SoyKB stores information about genes/proteins, miRNAs/sRNAs, metabolites, SNPs, plant introduction (PI lines) and traits. It handles the management and integration of soybean genomics and multi-omics data along with gene function annotations, biological pathway and trait information. It has many useful tools including gene family search, multiple gene/metabolite analysis, motif analysis tool, protein 3D structure viewer and data download and upload capacity. It has a user-friendly web interface together with genome browser and pathway viewer, which displays data in an intuitive manner to the soybean researchers, breeders and consumers. The QTLs, SNP, GWAS and traits information is seamlessly integrated in our newly developed suite of tools for the In Silico Breeding Program. It allows integration and extraction of the data in a tabular format as well as graphical visualization in our in-house Chromosome Visualizer. It also supports integration and visualization of Genotype by Sequencing (GBS) data for molecular breeding and phenotypic inferences. In addition, SoyKB now has capacity for incorporation of DNA methylation data and fast neutron mutation datasets. It is also linked seamlessly with P3DB for phosphorylation data. We have also incorporated suite of tools for differential expression analysis for microarray, transcriptomics RNA-seq, proteomics and metabolomics datasets. It includes access to gene lists, Venn diagrams, Volcano plots, functional annotations and pathway analysis. SoyKB is now powered by the iPlant Cyber-Infrastructure. The website is hosted on the iPlant’s advanced computing infrastructure established to leverage the data analysis capabilities. | ||||
| Organism(s) coveredNCBI Taxonomy names and IDs covered by the database | Glycine max (3847) | ||||
| Tag - TargetTag to indicate targets for this database such as genome and protein |
Genome/Gene
cDNA/EST
Genetic variation
Epigenetics
DNA
RNA
Protein
Carbohydrate
Lipid
Metabolite
Chemical compound
Drug
Cell/Organelle
Organism
Health/Disease
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| Tag - Information typeTag to indicate information types for this database such as sequence and structure |
Phenotype
Bioresource
Method
Ontology/Terminology/Nomenclature
Environment
Sequence
3D structure
Chemical structure
Expression
Localization
Geographic Distribution
Interaction/Pathway
Taxonomy
Classification
Image/Movie
Bibliography/Documents
Portal
Repository
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| Reference(s) - PubMed ID/DOIPubMed IDs/DOI for papers related to the database |
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| Language(s)Languages in which the contents of the database are displayed | English | ||||
| Operational statusOperational status for the database | Active | ||||
| Link(s) to Downloadable dataLinks to downloadable data | ― | ||||
| Link(s) to MetaData of downloadable dataLinks to metadata of downloadable data | ― | ||||
| Link(s) to Terms of useLinks to terms of use of downloadable data | ― | ||||
| Link(s) to "How to use" | ― | ||||
| Contact information of database | ― | ||||
| Link(s) to API / SPARQL endpoint | ― | ||||
| Link to LSDB ArchiveLink to LSDB Archive | ― | ||||
| Link to MEDALS Database listLink to MEDALS Database list | ― | ||||
| Link to TogoTVLink to TogoTV | ― | ||||
| Link to FAIRsharingLink to FAIRsharing | https://fairsharing.org/10.25504/FAIRsharing.cr410r | ||||
| Similar databasesDatabases that are similar to this database. | |||||
| Record maintainerRecord maintainer | See the corresponding part in the FAIRsharing record | ||||
| Record sourceOrganization that originally created the record |
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| Date of creation of this recordDate of creation of this English record | 2019-03-28 | ||||
| Last update date of this recordLast update date of this English record | 2024-07-24 | ||||
| Record license | Creative Commons Attribution and Share-alike (CC-BY-SA) International 4.0 license |